Explore the vast range of titles available.

Responses of cells to stimuli are increasingly discovered to involve the binding of sequence-specific transcription factors outside of known target genes. We wanted to determine to what extent the genome-wide binding and function of a transcription factor are shaped by the cell type versus the stimulus. To do so, we induced the Heat Shock Response pathway in two different cancer cell lines with two different stimuli and related the binding of its master regulator HSF1 to nascent RNA and chromatin accessibility. Here, we show that HSF1 binding patterns retain their identity between basal conditions and under different magnitudes of activation, so that common HSF1 binding is globally associated with distinct transcription outcomes. HSF1-induced increase in DNA accessibility was modest in scale, but occurred predominantly at remote genomic sites. Apart from regulating transcription at existing elements including promoters and enhancers, HSF1 binding amplified during responses to stimuli may engage inactive chromatin. The authors compare the heat shock response between different cell lines and stimuli and reveal the genome-wide binding of its master transcription factor HSF1 as a platform for context-specific transcription activation.

● Premise of the study: Over 50% of bryophytes have separate sexes, and numerous transitions have occurred between combined and separate sexes. Polyploidy and hybridization is one proximate mechanism hypothesized to cause evolutionary transitions to hermaphroditism in bryophytes because sex is expressed at the haploid stage and in nonpolyploid dioecious species males have a single V chromosome and females a U. Hermaphroditism can arise if gametophytes of allopolyploids have both U and V chromosomes. We examined the association between polyploidy and hermaphroditism in the bryophyte genus Atrichum, which has species where gametophytes can be haploid, diploid, or triploid, and some species have hermaphroditic individuals. • Methods: We generated phylogenies of Atrichum from sequences of three plastid regions (rbcL, rps4, and trnL-trnF) and the second intron for the nuclear gene Leafy/Floricaula to further understand the relationships among haploid, diploid, and triploid species, and those with combined or separate sexes. • Key results: The existence of multiple sequences of Leafy/Floricaula in diploid and triploid, but not haploid, individuals is consistent with independent allopolyploid origins of the diploid and triploid species. Allopolyploidy was associated with a likely gain in hermaphroditism in triploid Atrichum undulatum and possibly diploid A. altecristatum, but not in the allopolyploid A. crispulum (diploid at the gametophyte level). • Conclusions: These results highlight a role for hybridization and polyploidy in sexual system evolution, but the presence of diploid (allopolyploid) dioecious species suggest that other factors may influence the maintenance of sexual systems after an evolutionary transition.

Lyme disease is caused by infection with the bacterium Borrelia burgdorferi (Bb), which is transmitted to humans by deer ticks. The infection manifests usually as a rash and minor systemic symptoms; however, the bacteria can spread to other tissues, causing joint pain, carditis, and neurological symptoms. Lyme neuroborreliosis presents itself in several ways, such as Bell's palsy, meningitis, and encephalitis. The molecular basis for neuroborreliosis is poorly understood. Analysis of the changes in the expression levels of messenger RNAs and non-coding RNAs, including microRNAs, following Bb infection could therefore provide vital information on the pathogenesis and clinical symptoms of neuroborreliosis. To this end, we used cultured primary human astrocytes, key responders to CNS infection and important components of the blood-brain barrier, as a model system to study RNA and microRNA changes in the CNS caused by Bb. Using whole transcriptome RNA-seq, we found significant changes in 38 microRNAs and 275 mRNAs at 24 and 48 hours following Bb infection. Several of the RNA changes affect pathways involved in immune response, development, chromatin assembly (including histones) and cell adhesion. Further, several of the microRNA predicted target mRNAs were also differentially regulated. Overall, our results indicate that exposure to Bb causes significant changes to the transcriptome and microRNA profile of astrocytes, which has implications in the pathogenesis, and hence potential treatment strategies to combat this disease.

Background Global RNA sequencing technologies have revealed widespread RNA polymerase II (Pol II) transcription outside of gene promoters. Small 5′-capped RNA sequencing (Start-seq) originally developed for the detection of promoter-proximal Pol II pausing has helped improve annotation of Transcription Start Sites (TSSs) of genes as well as identification of non-genic regulatory elements. However, apart from the most well studied genomes of human and mouse, mammalian transcription has not been profiled with sufficiently high precision. Results We prepared and sequenced Start-seq libraries from rat ( Rattus norgevicus ) primary neural progenitor cells. Over 48 million uniquely mappable reads from two independent biological replicates allowed us to define the TSSs of 7365 known genes in the rn6 genome, reannotating 2503 TSSs by more than 5 base pairs, characterize promoter-associated antisense transcription, and profile Pol II pausing. By combining TSS data with polyA-selected RNA sequencing, we also identified thousands of potential new genes producing stable RNA as well as non-genic transcripts representing possible regulatory elements. Conclusions Our study has produced the first Start-seq dataset for the rat. Apart from profiling transcription initiation, our data reaffirm the prevalence of Pol II pausing across the rat genome and indicate conservation of pausing mechanisms across metazoan genomes. We suggest that pausing location, at least in mammals, is constrained by a distance from initiation of transcription, whether it occurs at or outside of a gene promoter. Abundant antisense transcription initiation around protein coding genes indicates that Pol II recruited to the vicinity of a promoter is distributed to available start sites of transcription at either DNA strand. Transcriptome profiling of neural progenitors presented here will facilitate further studies of other rat cell types as well as other organisms.

Whole genome sequencing (WGS) at high-depth (30X) allows the accurate discovery of variants in the coding and non-coding DNA regions and helps elucidate the genetic underpinnings of human health and diseases. Yet, due to the prohibitive cost of high-depth WGS, most large-scale genetic association studies use genotyping arrays or high-depth whole exome sequencing (WES). Here we propose a cost-effective method which we call “Whole Exome Genome Sequencing” (WEGS), that combines low-depth WGS and high-depth WES with up to 8 samples pooled and sequenced simultaneously (multiplexed). We experimentally assess the performance of WEGS with four different depth of coverage and sample multiplexing configurations. We show that the optimal WEGS configurations are 1.7–2.0 times cheaper than standard WES (no-plexing), 1.8–2.1 times cheaper than high-depth WGS, reach similar recall and precision rates in detecting coding variants as WES, and capture more population-specific variants in the rest of the genome that are difficult to recover when using genotype imputation methods. We apply WEGS to 862 patients with peripheral artery disease and show that it directly assesses more known disease-associated variants than a typical genotyping array and thousands of non-imputable variants per disease-associated locus.

BACKGROUND AND AIMS: Evolutionary transitions between separate and combined sexes have frequently occurred across various plant lineages. In mosses, which are haploid-dominant, evolutionary transitions from separate to combined sexes are often associated with genome doubling. Polyploidy and hermaphroditism have strong effects on the inbreeding depression of a population, and are subsequently predicted to affect the mating system. METHODS: We tested the association between ploidy (haploid, diploid or triploid gametophytes) and mating system in 21 populations of Atrichum undulatum sensu lato, where sex ratios vary widely. For each population, we measured the sex ratio, estimated selfing rates using allozyme markers and determined the level of ploidy through flow cytometry. KEY RESULTS: Hermaphrodites in A. undulatum were either diploid or triploid. However, many diploid populations were strictly separate-sexed, suggesting that hermaphroditism is not a necessary result of genome doubling. Levels of selfing were strongly supported as being greater than zero in one population with strictly separate-sexed individuals, and one-third of populations with hermaphrodites. CONCLUSIONS: Although hermaphrodites are associated with triploidy, hermaphroditism is not a necessary outcome of genome duplication. Hermaphroditism, but not genome duplication alone, increased estimated selfing rates, probably due to the occurrence of selfing within a gametophyte. Thus, genome duplication can influence the mating system and the associated evolution and maintenance of reproductive traits.

Populations of the moss Atrichum undulatum contain females, males, and hermaphrodites, and hermaphrodites can have sex organs in close proximity or spatially separated across branches. Here we ask whether differences in gender influence selfing rates or progeny fitness. We used allozyme electrophoresis to measure selfing rates of female and hermaphrodite gametophytes. We measured size and spore number of sporophytes from females and hermaphrodites and germination, survival, and photosynthetic capacity of their gametophytes grown on medium with supplemental nutrients or only with tap water to simulate a harsher environment. Females showed no significant selfing between sibling gametophytes. Significant within-gametophyte selfing was found in hermaphrodites with minimal spatial separation of male and female sex organs. Parental gender did not influence sporophyte size, but sporophytes from females contained slightly more spores. After 6 mo, only progeny from females survived on tap water media. When progeny were transplanted onto tap water media, progeny of females had greater photosynthetic capacity but also higher nonphotochemical quenching than that of hermaphrodites, resulting in realized photosynthetic rates similar to those of hermaphrodites. While the observed fitness differences are small, they suggest that there may be selection on sexual systems in A. undulatum, perhaps through either increased provisioning of resources to progeny by females or gametophytic inbreeding depression following selfing in hermaphrodites.

To better understand how gene transcription is controlled under different physiological and environmental conditions, we assessed transcription and methylation responses in a vertebrate system (salmon) where growth can be manipulated in response to growth hormone transgenesis or under satiated, feed-deprived, and re-fed experimental conditions. In both transgenic and non-transgenic liver tissue, methylation of gene promoters was negatively associated with transcription at all measured times. However, the changes in promoter methylation among time-points did not generally correlate with changes in gene transcription among treatments. The results from this study suggest that only a subset of genes are readily responsive to changes in promoter methylation for a given environmental shift such as feed-deprivation or a physiological shift such as growth hormone transgenesis (i.e., genotype-by-environment interactions). The present study also reveals the complexity of how one tissue responds to alterations in internal changes in physiology (growth modification by growth hormone transgenesis; genotype), external environmental conditions (food availability; environment), and their interactions (genotype-by-environment effects).

Populations of the mossAtrichum undulatumcontain females, males, and hermaphrodites, and hermaphrodites can have sex organs in close proximity or spatially separated across branches. Here we ask whether differences in gender influence selfing rates or progeny fitness. We used allozyme electrophoresis to measure selfing rates of female and hermaphrodite gametophytes. We measured size and spore number of sporophytes from females and hermaphrodites and germination, survival, and photosynthetic capacity of their gametophytes grown on medium with supplemental nutrients or only with tap water to simulate a harsher environment. Females showed no significant selfing between sibling gametophytes. Significant within-gametophyte selfing was found in hermaphrodites with minimal spatial separation of male and female sex organs. Parental gender did not influence sporophyte size, but sporophytes from females contained slightly more spores. After 6 mo, only progeny from females survived on tap water media. When progeny were transplanted onto tap water media, progeny of females had greater photosynthetic capacity but also higher nonphotochemical quenching than that of hermaphrodites, resulting in realized photosynthetic rates similar to those of hermaphrodites. While the observed fitness differences are small, they suggest that there may be selection on sexual systems inA. undulatum, perhaps through either increased provisioning of resources to progeny by females or gametophytic inbreeding depression following selfing in hermaphrodites.

Viral infection, particularly respiratory syncytial virus (RSV), causes inflammation in the bronchiolar airways (bronchial wall thickening, also known as bronchiolitis), reducing airflow through the bronchioles. This bronchial wall thickening is a common pathophysiological feature in RSV infection, but it causes more fatalities in infants than in children and adults. However, the molecular mechanism of RSV-induced bronchial wall thickening remains unknown, particularly in healthy adults. RSV infection in the airway epithelium of healthy adult bronchial cells reveals RSV-infects primarily ciliated cells. RSV infection expands the cell cytoskeleton substantially without compromising epithelial membrane integrity and ciliary functions. The RSV-induced actin cytoskeleton expansion increases ununiformly epithelial height, and cytoskeletal (actin polymerization), immunological (INF-L1, TNF-α, IP10/CXCL10), and viral (NS2) factors are probably responsible. Interestingly, RSV-infected cell cytoskeleton’s expansion resembles a noncanonical inflammatory phenotype, which contributes to bronchial wall thickening, and is termed cytoskeletal inflammation. RSV infects everyone. Although RSV-induced fatal pathophysiology (e.g., bronchiolitis) is more common in infants than adults, this bronchiolitis (or bronchial wall thickening) is common in the lower respiratory tract due to RSV infection in all ages. To determine the molecular mechanism of RSV-induced bronchial wall thickening, we infected in vitro adult airway epithelium with RSV. We found that RSV-infection induced a substantial actin-cytoskeleton expansion, consequently increased the height of the epithelium. We identified actin polymerization, secretion of proinflammatory cytokines and chemokines, and viral proteins contribute to the RSV-induced cytoskeletal expansion. Our results suggest that RSV-induces a novel noncanonical epithelial host response termed cytoskeletal inflammation, which may contribute to bronchial wall thickening.